def trigger(db, roots):
"""Queue events for completed analyses."""
mip_analyses = traverse(roots)
for mip_analysis in mip_analyses:
owner = mip_analysis.instance_tags[0]
if owner == 'cust000':
logger.debug("dismissing cust000 case: ", mip_analysis.family_id)
continue
case_id = "{}-{}".format(owner, mip_analysis.family_id)
try:
case_obj = db.case(case_id)
except NoResultFound:
logger.warn("case not found in database: %s", case_id)
continue
should_upload = (
(case_obj.uploaded_at is None) or
(mip_analysis.analyzed_at > case_obj.uploaded_analysis)
)
if should_upload:
logger.info("queue analysis for upload: %s", case_id)
visualize.dispatch(db, case_id, variant_type='clinical')
else:
logger.debug("case already uploaded")
def trigger(db, scout_db):
for category, scout_case in crawl(scout_db):
case_id = "{}-{}".format(scout_case.owner, scout_case.display_name)
if category == 'research':
logger.info("queueing %s for research upload", case_id)
visualize.dispatch(db, case_id, variant_type='research')
elif category == 'rerun':
logger.info("queueing %s for re-analysis", case_id)
analyze.dispatch(db, case_id)
elif category == 'archive':
logger.info("queueing %s for archive", case_id)
try:
familydir.dispatch_archive(db, case_id)
except NoResultFound as error:
logger.warn("case not found in database: %s", case_id)
def upload(case_id):
"""Upload research list for a case."""
variant_type = request.form.get('variant_type', 'clinical')
visualize.dispatch(db, case_id, variant_type)
return redirect(request.referrer)
